From 58c4f261dec50aa024a27231ca2a4ce1f22ae662 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Wed, 11 Feb 2015 16:50:25 -0500 Subject: [PATCH 1/3] Fix for resetting repository metadata in the toolshed via UI (pass resetting_all_metadata_on_repository=True flag). --- lib/galaxy/webapps/tool_shed/controllers/repository.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py index 9d8bc5ab660..56650debd36 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2763,7 +2763,8 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ): repository = suc.get_repository_in_tool_shed( trans.app, id ) rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, user=trans.user, - repository=repository ) + repository=repository, + resetting_all_metadata_on_repository=True ) rmm.reset_all_metadata_on_repository_in_tool_shed() rmm_metadata_dict = rmm.get_metadata_dict() rmm_invalid_file_tups = rmm.get_invalid_file_tups() @@ -2784,7 +2785,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ): @web.expose def reset_metadata_on_my_writable_repositories_in_tool_shed( self, trans, **kwd ): - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user, resetting_all_metadata_on_repository=True ) if 'reset_metadata_on_selected_repositories_button' in kwd: message, status = rmm.reset_metadata_on_selected_repositories( **kwd ) else: From 511465bc8560ab043675da3a25271c5aadeb9508 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Wed, 11 Feb 2015 17:31:49 -0500 Subject: [PATCH 2/3] Always add sample file info to metadata, not only during initial creation.. --- lib/tool_shed/metadata/metadata_generator.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/tool_shed/metadata/metadata_generator.py b/lib/tool_shed/metadata/metadata_generator.py index 81d5a62bdf9..0cf1fd40dc7 100644 --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -853,7 +853,7 @@ class MetadataGenerator( object ): if tool_path and relative_install_dir: if relative_path_to_sample_file.startswith( os.path.join( tool_path, relative_install_dir ) ): relative_path_to_sample_file = relative_path_to_sample_file[ len( tool_path ) + 1 :] - sample_file_metadata_paths.append( relative_path_to_sample_file ) + sample_file_metadata_paths.append( relative_path_to_sample_file ) return sample_file_metadata_paths, sample_file_copy_paths def handle_repository_elem( self, repository_elem, only_if_compiling_contained_td=False ): From 2332e180cc67aefa56b3c481d3b734205b12bcbe Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Wed, 11 Feb 2015 17:36:05 -0500 Subject: [PATCH 3/3] When resetting repository metadata in the toolshed, don't overwrite the already set relative_install_dir. --- lib/tool_shed/metadata/repository_metadata_manager.py | 1 - 1 file changed, 1 deletion(-) diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py index f4166388731..5c7f8a5e7a1 100644 --- a/lib/tool_shed/metadata/repository_metadata_manager.py +++ b/lib/tool_shed/metadata/repository_metadata_manager.py @@ -834,7 +834,6 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): if cloned_ok: log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) ) self.set_changeset_revision( str( repo.changectx( changeset ) ) ) - self.set_relative_install_dir( work_dir ) self.set_repository_files_dir( work_dir ) self.generate_metadata_for_changeset_revision() if self.metadata_dict: